Under complex flight conditions, it is hard to realize the trajectory tracking control of the quadrotor with unmeasurable speed. Considering the existence of unknown external disturbance and uncertain model parameters, the trajectory tracking control method based on an extended state observer is proposed. Firstly, the integral backstepping tracking controller is designed to reduce the steady state error of the system, and the state extended observer is introduced to estimate the unknown speed of the system. Then, the disturbance and the uncertainty of model parameters are estimated in real time and compensated accordingly. Finally, the Lyapunov function is utilized to prove the stability of the control system. Experiments are implemented on the Qball2 platform of Quanser′s quadrotor. Results show that the trajectory tracking controller based on the extended state observer can estimate the unknown speed in the trajectory tracking control process effectively. It can also solve the problem of unknown external disturbance and model parameter uncertainty. The adaptability to the environment can be enhanced. The robustness of the quadrotor to unknown disturbances and the accuracy of trajectory tracking control are improved effectively.